Yes, friendly fire is a bother - after each battle, I check my losses against the enemies kills and count it as a good result if friendly fire losses are less than enemy kills. I now try to lead with archers/velites, rather than have them at the rear (as in MTW and STW). I suspect this is more historical - I was surprised in MTW that the crossbows and arbalests could shoot overhead with impunity.

With archers, their range is pretty good so you can sometimes use them profitably without being charged. And to be honest, if the AI does rush you that is pretty realistic too - better than just standing there to die on the city plaza. In MTW, I found archers almost alone could win battles for me - in RTW, they are more lethal but nonetheless account for a smaller proportion of casualties (as the AI closers more often and faster).

With velites, skirmishing is a problem but can nonetheless be used to provoke the enemy. I've noticed the AI try to charge my velites - they run behind my lines, the enemy looks at the wall of hastati and stops, often retreats. They then suffer from the hastati's fire at will pila and the velites come back after them. Javelins seem pretty powerful when they do get off.

I'm still in too minds about the units' charge speed - yes, it is fast and so emphasises initial deployment. But maybe this is realistic? The game abstracts from command and control, so maybe this is a way of bringing back in those considerations. To expect your units to immediately ceasefire seems rather realistic (consider "friendly fire" losses in the Gulf Wars, when command and control was far better than on an ancient battlefield).